Search results for "look through"

Re: [cctbxbb] CBF compositing

by Graeme.Winter＠diamond.ac.uk

Hi Frank, OK, so we have done something recently which I think would be very similar, converting tiff files and "dat" files (don't ask) to full 'n' proper cbf files. It worked sensibly and would work in your case, but as you point out it would involve some post processing. In this example however the postprocessing was done by cbflib, which makes it a little more kosher. In essence, the program does this: - read tiff files -> numpy arrays -> sum - read dat file - write cbf header with empty image using template and dat file contents - read / write this file through cbflib adding the image data in flight You should be able to do this all in one go, looking at pycbf_test4.py in the new distribution of cbflib / pycbf, but you may find it a bit of a fiddle constructing the full cbf file ab initio. Cheerio, Graeme -----Original Message----- From: cctbxbb-bounces(a)phenix-online.org [mailto:[email protected]] On Behalf Of Frank Murphy Sent: 03 December 2012 13:19 To: cctbx mailing list Subject: Re: [cctbxbb] CBF compositing Graeme, Unfortunately, my intent is to write out the image as a proper CBF. Your email is exactly correct, as I was at first quite happy to find how simple it was to add the images together, but then disappointed as I have struggled writing out a proper CBF in one step. I, of course, can write the CBF out and then hack the header, but this wastes a lot of time, having to effectively write a CBF twice. I was able to write a header and CBF data separately and then concatenate them, but the header for the CBF data file needs edited... Frank On Dec 3, 2012, at 5:01 AM, <Graeme.Winter(a)diamond.ac.uk> wrote: > Hi Frank, > > It would be easy to write one, as pycbf is included in there as is some code to unpack the byte-offset compression quickly in iotbx.detectors - > > from iotbx.detectors import ImageFactory > > image = ImageFactory(filename) > image.read() > image.get_raw_data() > > You would however need to create and pack the data to a new CBF file, which IIRC requires some new additions to the pycbf bindings - I asked Herbert B about this a while back and he needed to make some patches as it was not generally possible. That said, what I was after was creating a full cbf not e.g. miniCBF. > > Adding the new version to a live version of cctbx/python is easy enough. > > I take it as a given that this is for visualizing - you're not too worried about the image headers? Otherwise this will be somewhat more tricky. > > Email from Herbert B follows. It went to the imgCIF mailing list so is public already :o) > > Best wishes, > > Graeme > > ------------- > > > Dear Graeme, > > I have made a new example that uses setters and writes a byte-offset compressed image. Testing revealed some bugs in the wrapper for some of the setters, so I have also updated the release kit. The whole thing is available on the CBFlib_bleeding_edge svn on sourceforge as well as a release kit > > http://downloads.sf.net/cbflib/CBFlib-0.9.2.6.tar.gz > > Please give it a try and take a look at pycbf/pycbf_test4.py for an example of writing a byte-offset CBF. Let me know if it does what you need. If not, tell me what is missing or wrong and I'll be happy to fix things and add more pycbf examples to the kit. > > Regards, > Herbert > > P.S. This was a very useful question because it relate to testing the HDF5 changes. > > -----Original Message----- > From: cctbxbb-bounces(a)phenix-online.org [mailto:[email protected]] On Behalf Of Frank Murphy > Sent: 01 December 2012 14:22 > To: cctbx mailing list > Subject: [cctbxbb] CBF compositing > > Hello, > > Does anyone have a CCTBX-based method for compositing multiple CBFs to a single image a la merge2cbf? > > Thanks in advance, > Frank Murphy > > > > _______________________________________________ > cctbxbb mailing list > cctbxbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/cctbxbb > > -- > This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. > Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. > Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. > Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom > > > > > _______________________________________________ > cctbxbb mailing list > cctbxbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/cctbxbb Frank Murphy frankvmurphy(a)gmail.com _______________________________________________ cctbxbb mailing list cctbxbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/cctbxbb -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

13 years, 2 months

Re: [phenixbb] Discrepancy between Phenix GUI and command line for MR

by Randy John Read

Hi, Thanks for sending the log files! The jobs turn out not actually to be identical. The GUI automatically chose to use the intensity data (which is what we prefer for use in Phaser) whereas your job run from a script is using amplitude data. The issue I alluded to earlier occurs only for intensity data, because the analysis of those data involves applying different equations, which use a special function (tgamma from the Boost library). For some reason I don’t understand, when the Intel version of the tgamma algorithm is computed using the Rosetta functionality to run it on an ARM processor, it’s much much slower than other calculations. Just last week (right after I finally got an M2 MacBook Pro), we tracked this down and replaced the calls to Boost tgamma with alternative code, and that problem should exist any more. You can use it already in Phenix by getting a recent nightly build, and I’ve asked the CCP4 people to compile a new version of Phaser and release it as an update to CCP4 as well. Best wishes, Randy > On 4 Jul 2023, at 12:05, Xavier Brazzolotto <xbrazzolotto(a)gmail.com> wrote: > > For information > > Apple M2 running Ventura 13.4.1 with 64 Go memory > Phenix 1.20.1-4487 (Intel one). > > I’ve run MR of the same dataset (2.15A - I422) with the same model both with the command line and through the GUI. > > Command line (phenix.phaser) : 48 secs. > GUI (Phaser-MR simple one component interface): 18 mins ! > > In copy the two log files if this helps > > > > > Le 4 juil. 2023 à 12:54, Luca Jovine <luca.jovine(a)ki.se> a écrit : > > > > Hi Xavier and Randy, I'm also experiencing the same on a M2 Mac! > > -Luca > > > > -----Original Message----- > > From: <phenixbb-bounces(a)phenix-online.org <mailto:[email protected]>> on behalf of Xavier Brazzolotto <xbrazzolotto(a)gmail.com <mailto:[email protected]>> > > Date: Tuesday, 4 July 2023 at 12:38 > > To: Randy John Read <rjr27(a)cam.ac.uk <mailto:[email protected]>> > > Cc: PHENIX user mailing list <phenixbb(a)phenix-online.org <mailto:[email protected]>> > > Subject: Re: [phenixbb] Discrepancy between Phenix GUI and command line for MR > > > > > > Hi Randy, > > > > > > Indeed I’m running Phenix on a brand new M2 Mac. > > I will benchmark the two processes (GUI vs command line) and post them here. > > > > > >> Le 4 juil. 2023 à 12:32, Randy John Read <rjr27(a)cam.ac.uk <mailto:[email protected]>> a écrit : > >> > >> Hi Xavier, > >> > >> We haven’t noticed that, or at least any effect is small enough not to stand out. There shouldn’t be a lot of overhead in communicating with the GUI (i.e. updating the terse log output and the graphs) but if there is we should look into it and see if we can do something about it. > >> > >> Could you tell me how much longer (say, in percentage terms) a job takes when you run it through the GUI compared to running the same job outside the GUI on the same computer? Also, it’s possible the architecture matters so could you say which type of computer and operating system you’re using? If it’s a Mac, is it one with an Intel processor or an ARM (M1 or M2) processor? (By the way, we finally managed to track down and fix an issue that cause Phaser to run really slowly on an M1 or M2 Mac when using the version compiled for Intel, once I got my hands on a new Mac.) > >> > >> Best wishes, > >> > >> Randy > >> > >>> On 4 Jul 2023, at 10:44, Xavier Brazzolotto <xbrazzolotto(a)gmail.com <mailto:[email protected]>> wrote: > >>> > >>> Dear Phenix users > >>> > >>> I’ve noticed that molecular replacement was clearly slower while running from the GUI compared to using the command line (phenix.phaser). > >>> > >>> Did you also observe such behavior? > >>> > >>> Best > >>> Xavier > >>> _______________________________________________ > >>> phenixbb mailing list > >>> phenixbb(a)phenix-online.org <mailto:[email protected]> > >>> http://phenix-online.org/mailman/listinfo/phenixbb <http://phenix-online.org/mailman/listinfo/phenixbb> > >>> Unsubscribe: phenixbb-leave(a)phenix-online.org <mailto:[email protected]> > >> > >> > >> ----- > >> Randy J. Read > >> Department of Haematology, University of Cambridge > >> Cambridge Institute for Medical Research Tel: +44 1223 336500 > >> The Keith Peters Building > >> Hills Road E-mail: rjr27(a)cam.ac.uk <mailto:[email protected]> > >> Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk > >> > > > > > > > > > > _______________________________________________ > > phenixbb mailing list > > phenixbb(a)phenix-online.org <mailto:[email protected]> > > http://phenix-online.org/mailman/listinfo/phenixbb <http://phenix-online.org/mailman/listinfo/phenixbb> > > Unsubscribe: phenixbb-leave(a)phenix-online.org <mailto:[email protected]> > > > > > > > > När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://ki.se/medarbetare/integritetsskyddspolicy>. > > > > > > Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI’s processing of personal data here<https://ki.se/en/staff/data-protection-policy>. > > <command_line_PHASER.log><GUI_phaser.log> ----- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: +44 1223 336500 The Keith Peters Building Hills Road E-mail: rjr27(a)cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk

2 years, 7 months

[phenixbb] Re: for autobuild full sequence?

by Pavel Afonine

Hi James, Yes, that makes sense, and it’s what I suspected. Creating a string of residues that matches your sequence is, as I mentioned, a ten-minute exercise in CCTBX. However, ensuring that it folds within the allowed volume, avoids self-clashes, and meets other geometric quality metrics is a more complex challenge—but not impossible. My approach would be to create a map where all voxels occupied by existing atoms have negative values. Then, assuming the start and end points of your chain are known, I’d generate a rough path through non-negative voxels. From there, a round of real-space simulated annealing could refine the structure. But that’s starting to sound like a full project now! Pavel On 4/1/25 13:23, James Holton wrote: > Yes, but I don't want it to clash with other molecules in the unit > cell, including itself. > > When I was an undergrad, Steve Mayo called this an "amorphous > builder". Trivial in concept, but you need to do a "bump check" after > adding each atom, and then have a plan for what to do if you hit a bump. > > Make sense? > > -James > > > On 4/1/2025 1:10 PM, Pavel Afonine wrote: >> Hi James, >> >> Are you just looking to string residues together in a line from start >> to end according to your sequence? That’s a quick 10-minute exercise >> using CCTBX, but I suspect that’s not exactly what you need. >> >> Pavel >> >> On 4/1/25 12:28, Tom Terwilliger wrote: >>> Hi James, >>> I think there is no way to force AutoBuild to build a full sequence >>> when there is no density. >>> All the best, >>> Tom T >>> >>> >>> On Tue, Apr 1, 2025 at 10:26 AM James Holton <jmholton(a)lbl.gov> wrote: >>> >>> Hey all, >>> >>> Don't worry, nothing is funny today. I have a real question: >>> >>> Is there a way to force phenix.autobuild to build in the entire >>> sequence? As in: the full length of the actual molecule that is >>> in the >>> crystal, such as what is supposed to go into SEQRES, regardless of >>> "visible" density? I am trying to come up with a pipeline for >>> prepping >>> MD simulations of protein crystals. It seems proper to me that the >>> molecule being simulated should be the actual molecular species, >>> disordered bits an all. However, we don't seem to have good >>> technology >>> for building protein chains into "nothingness". Yes, I know >>> Alphafold is >>> a thing, but it is rubbish at clashes in the context of a crystal. >>> >>> I mean, I could write something, but does this tool already exist? >>> >>> Cheers, and happy Tuesday, >>> >>> -James Holton >>> MAD Scientist >>> >>> >>> _______________________________________________ >>> phenixbb mailing list -- phenixbb(a)phenix-online.org >>> To unsubscribe send an email to phenixbb-leave(a)phenix-online.org >>> Unsubscribe: phenixbb-leave@%(host_name)s >>> >>> >>> >>> -- >>> Thomas C Terwilliger >>> Laboratory Fellow, Los Alamos National Laboratory >>> Senior Scientist, New Mexico Consortium >>> 100 Entrada Dr, Los Alamos, NM 87544 >>> Email: tterwilliger(a)newmexicoconsortium.org >>> Tel: 505-431-0010 >>> >>> >>> _______________________________________________ >>> phenixbb mailing list --phenixbb(a)phenix-online.org >>> To unsubscribe send an email tophenixbb-leave(a)phenix-online.org >>> Unsubscribe: phenixbb-leave@%(host_name)s >

10 months, 1 week

Re: [phenixbb] Molecular replacement with fixed solution

by Muhammed bashir Khan

Thanks Randy for your detail reply. Its worked out.. On Fri, January 16, 2015 21:06, Randy Read wrote: > Hi, > > There are two ways to do this, and I’ve just tested them both using the > beta-lactamase:BLIP tutorial from the Phenix distribution. > > 1. The easy way, which is what users are generally meant to do. Define > all the necessary background information (data, both ensembles: beta and > blip, composition with sequence files). Specify one search for one > component, e.g. beta. When this finishes, go to the main “Input and > general options” pane of the GUI and, in the “Use partial solution from > previous job” pulldown, choose the job that placed the beta component. > Now go to the “Search procedure” pane and uncheck “beta” for the search > model and check “blip” instead. Run the search, and it will place the > blip component in the context of the already placed beta-lactamase > component. This could go wrong if the user is obsessively tidy and > deletes the definition for the “beta” ensemble between the first and > second jobs, because the partial solution information specifies how to > place a defined ensemble (which therefore still has to be defined), but it > does not store the placed ensemble. > > 2. The harder way, which is probably what you were trying to do. After > placing the first component, define a new ensemble, giving the PDB file > from the phaser subdirectory created in the first search (I called this > ensemble “beta_placed”). For this one, check the box labelled “Ensemble > is fixed partial solution”. Again, in the “Search procedure” pane, > uncheck “beta” and check “blip”, then run the search. Note that you’re > not specifying any search for the already placed component. This way of > doing things was really only created so people could come in halfway > through a structure solution with another molecular replacement program, > not as the way you would choose to do it with Phaser. > > Actually, the very easiest way, which I hope most users do by default, is > to decide at the beginning what you are hoping to find in the structure > solution and specify all the copies of all the components you’re looking > for in one job. That approach gives Phaser the most flexibility to use an > adaptive search strategy. So, in the tutorial, users are instructed to > set up two searches in the one job, searching for both “beta” and “blip”. > > Let me know if that doesn’t clarify things. > > Randy Read > > ----- > Randy J. Read > Department of Haematology, University of Cambridge > Cambridge Institute for Medical Research Tel: +44 1223 336500 > Wellcome Trust/MRC Building Fax: +44 1223 336827 > Hills Road > E-mail: rjr27(a)cam.ac.uk > Cambridge CB2 0XY, U.K. > www-structmed.cimr.cam.ac.uk > > On 16 Jan 2015, at 18:56, Muhammed bashir Khan > <muhammad.bashir.khan(a)UNIVIE.AC.AT> wrote: > >> Hi There; >> >> I want to solve the structure with molecular replacement using phaser in >> phenix GUI. When I get solution from the one, how I can use as it as >> already solution using phenix in the next run. I use the "ensamble is >> fixed partial solution" but seems its not working. Any suggestion will >> be >> highly appreciated. Thanks >> >> Regards >> >> >> -- >> Muhammad Bashir Khan >> ************************************************** >> Department for Structural and Computational Biology >> Max F. Perutz Laboratories >> University of Vienna >> Campus Vienna Biocenter 5 >> A-1030 Vienna >> Austria >> >> Austria >> >> Phone: +43(1)427752224 >> Fax: +43(1)42779522 >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb > > -- Muhammad Bashir Khan ************************************************** Department for Structural and Computational Biology Max F. Perutz Laboratories University of Vienna Campus Vienna Biocenter 5 A-1030 Vienna Austria Austria Phone: +43(1)427752224 Fax: +43(1)42779522

11 years

Re: [cctbxbb] WSL2 (was: Windows icc builds)

by Viktor Bengtsson

Hi Graeme and Kay, I'll add my 2 cents to this as well. I have been using WSL with VcXsrv since February 2018 for all Linux-primary software needs and DIALS in particular. Before that I tried using DIALS both on Ubuntu through Virtualbox and compiled for Windows directly on my computer. Based on my experience, I would suggest reconsidering if native Windows support is still relevant. At the same time I do know that there are some parts that still don't really translate well into WSL2, so maybe a Windows native application still is worth the time. Otherwise a link to the xdswiki should be enough support, in particular once WSL2 can be installed on all Windows 10 computers with a simple "wsl --install" in PowerShell or CMD with admin privileges. The fact that the original github issue is based on the WSL2 version being faster than native Windows version also supports that WSL2 might be a better version of "Windows support". If the point of a Windows version is to make it simple to install for Windows users, then maybe it might be possible to write a installation script that performs all relevant steps, including installation of WSL2 if needed? tl;dr: I agree that WSL2 is a good enough solution, and would add vcxsrv as an additional option if you only want the Xserver and not the full MobaXterm. Kind regards, Viktor -----Original Message----- From: cctbxbb-bounces(a)phenix-online.org <cctbxbb-bounces(a)phenix-online.org> On Behalf Of Kay Diederichs Sent: den 26 maj 2021 21:33 To: cctbxbb(a)phenix-online.org Subject: [cctbxbb] WSL2 (was: Windows icc builds) Hi Graeme, I have no solution for this problem but I want to bring up the fact that WSL2 is very easy to install on current Windows10, and lets one run the Linux binaries (including graphics if you install MobaXterm which has an Xserver) quite efficiently. I have not run into a single problem when trying WSL2 with XDS and XDSGUI; my writeup is at https://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Installation#WS… . I think those who struggle with developing for Windows, including you, the Phenix team and the CCP4 team, might be able to save a lot of time/effort (and those who just use Windows would benefit in the long run by getting used to a Linux environment). Microsoft announced WSLg (the g stands for graphics) which provides an Xserver, but this currently requires Windows-Build 21362+ (Windows Insider Program). Give it a try! Just my 2 cents, Kay > Date: Wed, 26 May 2021 18:57:27 +0000 > From: "Winter, Graeme (DLSLtd,RAL,LSCI)" <Graeme.Winter(a)diamond.ac.uk> > To: cctbx mailing list <cctbxbb(a)phenix-online.org> > Subject: [cctbxbb] Windows icc builds > Message-ID: <6210D39B-96F7-493F-98D4-D1EDFCBE09A5(a)diamond.ac.uk> > Content-Type: text/plain; charset="utf-8" > > HI Folks > > Following from a DIALS issue about it being slow on Windows > > https://github.com/dials/dials/issues/1666 > > I have fallen into a rabbit hole and I am trying to build DIALS (and > hence cctbx) on Windows with the intel compilers from oneAPI - however > I keep stumbling over linking errors with e.g. undefined symbol > __floor > > Should I abandon hope or has someone done this? > > I know this is not a new path to tread as windows_icc was a defined > combination on the SConscripts > > I had had to hack some bits around a little presumably to accommodate > 2021 versions of icc compilers, but this felt like I was going down a > bad path > > Would welcome input from anyone who can help - currently windows DIALS > is a pretty poor relation > > It is noteworthy however that parallel operation does now appear to > work on Windows with easy mp :-) > > In other news - has anyone considered adding clang support with clang coming from conda? Could make for more consistency in the builds? I had a look at how one may go about doing this but rapidly found myself in SCons hell. > > Thanks in advance for any help & all the best Graeme > -- Kay Diederichs http://strucbio.biologie.uni-konstanz.de email: Kay.Diederichs(a)uni-konstanz.de Tel +49 7531 88 4049 Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz This e-mail is digitally signed. If your e-mail client does not have the necessary capabilities, just ignore the attached signature "smime.p7s".

4 years, 8 months

[phenixbb] PHENIX 1.24.1 beta now available

by Paul Adams

======================================================================= PHENIX 1.24.1 Beta Release ======================================================================= On behalf of the PHENIX development team I am happy to announce that the next general release version of PHENIX is now available. Binary installers for Linux, SGI and Tru64 platforms are available at our download site: http://phenix-online.org/download/ Current users of PHENIX should upgrade to this most recent release version. To obtain download instructions visit: http://phenix-online.org/phenix_request/ Documentation for PHENIX is available at: http://phenix-online.org/download/documentation/phenix/ There is a PHENIX mailing list at: http://www.phenix-online.org/mailman/listinfo/phenixbb/ There is a PHENIX wiki at: http://www.phenix-online.org/phenix_wiki Please consult the installer README file or online documentation for installation instructions. This is a beta test version, and we therefore look forward to feedback and bug reports from users. Please direct questions and problem reports to: help(a)phenix-online.org and bugs(a)phenix-online.org Commercial users interested in obtaining access to PHENIX should visit the PHENIX website for information about the PHENIX Industrial Consortium: http://www.phenix-online.org/ This version of PHENIX has three main user interfaces: command-line tools, strategies and wizards. Wizards are available under the Wizard tab in the PHENIX GUI, and are designed to complete a complex structure determination process, making automatic decisions when possible, but prompting the user for additional information when necessary. Strategies are available under the Strategy tab in the PHENIX GUI, and are networks of tasks constructed to perform higher-level functions. Version 1.24.1b of PHENIX includes: Wizards (in the PHENIX GUI and from the command-line) ===================================================== - AutoSol - automated structure solution (from processed data to a first map and model) using HySS, SOLVE, RESOLVE, and phenix.refine. - AutoMR - automated molecular replacement, using PHASER. Followed by automated model rebuilding using the AutoBuild wizard. - AutoBuild - automated model building or rebuilding combined with structure refinement, using RESOLVE and phenix.refine. - AutoLig - automated ligand fitting into difference density maps using RESOLVE once a complete protein model is available. Strategies (in the PHENIX GUI) ============================== - Ligand screening against the top 200 ligands in the PDB, using RESOLVE. - Structure solution (MAD/SAD and SIR(AS)/MIR(AS)) combining HySS, SOLVE and RESOLVE. - Phase improvement using maximum likelihood methods in RESOLVE. - Model building using TEXTAL or RESOLVE. Command-line tools ================== - mmtbx.xtriage (comprehensive data quality assessment, including twin analysis) - iotbx.reflection_statistics (analysis of diffraction data) - mmtbx.fest (FA value calculation) - phenix.hyss (anomalous substructure determination) - textal.build (automated model building with TEXTAL) - elbow.builder (generation of ligand coordinates and restraints) - phenix.refine (automated structure refinement) - phenix.geometry_minimization (regularize a structure) - phenix.solve (solve) - phenix.resolve (resolve) - phenix.resolve_pattern (resolve_pattern) - iotbx.mtz.dump (write useful information about a MTZ file) - iotbx.pdb.hierarchy (write useful information about a PDB file) Citing PHENIX ============= If you use PHENIX for solving a structure please cite this publication: PHENIX: building new software for automated crystallographic structure determination P.D. Adams, R.W. Grosse-Kunstleve, L.-W. Hung, T.R. Ioerger, A.J. McCoy, N.W. Moriarty, R.J. Read, J.C. Sacchettini, N.K. Sauter and T.C. Terwilliger. Acta Cryst. D58, 1948-1954 (2002). PHENIX Developers ================= Lawrence Berkeley National Laboratory - Paul D. Adams - Pavel Afonine - Ralf W. Grosse-Kunstleve - Nigel W. Moriarty - Nicholas K. Sauter - Peter H. Zwart Los Alamos National Laboratory - Tom C. Terwilliger - Li-Wei Hung - Thiru Radhakannan University of Cambridge - Randy J. Read - Airlie J. McCoy - Laurent C. Storoni Texas A&M University - Jim C. Sacchettini - Tom R. Ioerger - Kresha Gopal - Lalji Kanbi - Erik McKee - Reetal K. Pai - Tod D. Romo - Jacob N. Smith Acknowledgements ================ We are very grateful to the following for making code or libraries available to us: - Alexei Vagin and Garib Murshudov for the CCP4 Monomer Library. - The CCP4 developers for making the MTZ library available to us. - Kevin Cowtan for contributing to the cctbx reciprocal space asymmetric units. - David Abrahams for developing the Boost.Python library. Funding ======= The development of PHENIX is principally funded through the Protein Structure Initiative of the National Institute of General Medical Sciences (NIH) under grant P01GM063210. For further information about the Protein Structure Initiative please visit: http://www.nigms.nih.gov/psi/ We also acknowledge the generous support of the members of the PHENIX Industrial Consortium. For more details please visit: http://www.phenix-online.org/ ======================================================================= PHENIX 1.24.1 Beta Release ======================================================================= -- ========================================================== | Paul Adams, | | Senior Staff Scientist, Physical Biosciences Division | | Head, Berkeley Center for Structural Biology | | Deputy PI, Berkeley Structural Genomics Center | |--------------------------------------------------------| | Building 64, Room 248 | Lawrence Berkeley Laboratory, | | Tel: 510-486-4225 | 1 Cyclotron Road, | | FAX: 510-486-5909 | BLDG 64R0121, | | mailto:[email protected] | Berkeley, CA 94720, USA. | ==========================================================

19 years, 7 months

Re: [phenixbb] TRIED resolve ...NEED A BIGGER VERSION... message

by Tom Terwilliger

Hi Felix, Well almost. It will activate the right size if it exists in the distribution that you have. The normal extra_huge version is "isizeit = 36" which is 6 x the standard size. If that is not big enough autobuild will stop. I can provide bigger versions if you need them (and then they will automatically be used). All the best, Tom T Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: terwilliger(a)LANL.gov Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss On Jan 5, 2009, at 8:36 AM, Felix Frolow wrote: > Tom, does it mean that for structure of ANY size the right version > of RESOLVE will be activated now automatically? > If it does, it is very important improvement > FF > Dr Felix Frolow > Professor of Structural Biology and Biotechnology > Department of Molecular Microbiology > and Biotechnology > Tel Aviv University 69978, Israel > > Acta Crystallographica D, co-editor > > e-mail: mbfrolow(a)post.tau.ac.il > Tel: ++972 3640 8723 > Fax: ++972 3640 9407 > Cellular: ++972 547 459 608 > > On Jan 5, 2009, at 5:25 PM, Tom Terwilliger wrote: > >> Hi Ben, >> Yes, that is just FYI. There are a few sizes of resolve and this >> means the smallest wasn't big enough. I'll change the message so >> that it is more informative... >> All the best, >> Tom T >> >> >> >> Thomas C. Terwilliger >> Mail Stop M888 >> Los Alamos National Laboratory >> Los Alamos, NM 87545 >> >> Tel: 505-667-0072 email: terwilliger(a)LANL.gov >> Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov >> PHENIX web site: http:www.phenix-online.org >> ISFI Integrated Center for Structure and Function Innovation web >> site: http://techcenter.mbi.ucla.edu >> TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB >> CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss >> >> >> >> >> On Jan 5, 2009, at 8:09 AM, Ben Eisenbraun wrote: >> >>> >>> Howdy Phenixians, >>> >>> One of my users is running phenix.autobuild, and while it seems to >>> run >>> okay, the output contains this warning: >>> >>> TRIED resolve ...NEED A BIGGER VERSION... >>> >>> Looking through phenix/phenix/autosol/run_resolve.py, it seems >>> like this >>> is an informational message, but I'm not sure, so I figured I'd ask. >>> >>> Is this actually an error? >>> >>> This is phenix-1.3-final on OS X 10.5. >>> >>> Thanks. >>> >>> -ben >>> >>> -- >>> Ben Eisenbraun >>> Structural Biology Grid Harvard Medical >>> School >>> http://sbgrid.org http://hms.harvard.edu >>> _______________________________________________ >>> phenixbb mailing list >>> phenixbb(a)phenix-online.org >>> http://www.phenix-online.org/mailman/listinfo/phenixbb >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb

17 years, 1 month

Re: [phenixbb] calculate Fc for the whole unit cell from a Fc of a single symmetric unit.

by zhangh1＠umbc.edu

Thanks a lot! > We can expand reciprocal-space arrays, too, with the > cctbx.miller.array.expand_to_p1() > method. You can use it from the command line via > > phenix.reflection_file_converter --expand-to-p1 ... > > See also: > http://www.phenix-online.org/documentation/reflection_file_tools.htm > > Ralf > > > On Mon, Jul 11, 2011 at 10:56 AM, <zhangh1(a)umbc.edu> wrote: > >> Sorry I haven't got a chance to check my email recently. >> >> Yes, I meant expansion to P1. The thing is cctbx relies on the atomic >> model I think, but I only have model Fc available. >> >> Hailiang >> >> > I suspect what Hailang means is expansion into P1. >> > >> > I am sure this can be accomplished through some either existing or >> > easily coded cctbx tool. However, when I looked into a different task >> > recently that included P1 expansion as a step, I learned that SFTOOLs >> > can do this, albeit there was a bug there which caused trouble in >> > certain space groups (may be fixed by now so check if there is an >> > update). >> > >> > Hailang - if P1 expansion is what you need, I could share my own code >> as >> > well, let me know if that is something you want to try. >> > >> > Cheers, >> > >> > Ed. >> > >> > On Fri, 2011-07-08 at 14:44 -0700, Ralf Grosse-Kunstleve wrote: >> >> Did you get responses already? >> >> If not, could you explain your situation some more? >> >> We have algorithms that do the symmetry summation in reciprocal >> space. >> >> The input is a list of Fc in P1, based on the unit cell of the >> >> crystal. Is that what you have? >> >> Ralf >> >> >> >> On Wed, Jul 6, 2011 at 1:38 PM, <zhangh1(a)umbc.edu> wrote: >> >> Hi, >> >> >> >> I am wondering if I only have structure factors calculated >> >> from a single >> >> symmetric unit, is there any phenix utility which can >> >> calculate the >> >> structure factor for the whole unit cell given the symmetric >> >> operation or >> >> space group and crystal parameters? Note I don't have an >> >> atomic model and >> >> only have Fc. >> >> >> >> Thanks! >> >> >> >> Hailiang >> >> >> >> _______________________________________________ >> >> phenixbb mailing list >> >> phenixbb(a)phenix-online.org >> >> http://phenix-online.org/mailman/listinfo/phenixbb >> >> >> >> >> >> _______________________________________________ >> >> phenixbb mailing list >> >> phenixbb(a)phenix-online.org >> >> http://phenix-online.org/mailman/listinfo/phenixbb >> > >> > >> > _______________________________________________ >> > phenixbb mailing list >> > phenixbb(a)phenix-online.org >> > http://phenix-online.org/mailman/listinfo/phenixbb >> > >> > >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb >

14 years, 6 months

[phenixbb] Re: Simulate map from model

by Ricardo Righetto

Dear all, Thanks a lot for your replies! After playing a bit with the suggested command line programs I decided to follow Robert's suggestion and go the Python way, hoping to gain finer control of the options. I am using the attached Python script to calculate an exact map from a model, using electron scattering table. When running, for example, on 4v7t.cif I get a map that looks as follows (orthogonal central slices): [image: image.png] And the MRC header as read by IMOD is: RO image file on unit 1 : fourier_map.mrc Size= 32401 K Number of columns, rows, sections ..... 320 240 108 Map mode .............................. 2 (32-bit float) Start cols, rows, sects, grid x,y,z ... 0 0 0 108 240 320 Pixel spacing (Angstroms).............. 1.958 1.809 1.941 Cell angles ........................... 90.000 90.000 90.000 Fast, medium, slow axes ............... Z Y X Origin on x,y,z ....................... 0.000 0.000 0.000 Minimum density ....................... 0.0000 Maximum density ....................... 2.5699 Mean density .......................... 0.12004E-01 RMS deviation from mean................ 0.47980E-01 tilt angles (original,current) ........ 0.0 0.0 0.0 0.0 0.0 0.0 Space group,# extra bytes,idtype,lens . 19 0 0 0 1 Titles : Some text With these in mind, I have some questions: 1) If I understand correctly, the map contains exactly one unit cell as defined in the .cif file. How can I choose a different assembly to generate the map from? Say, biological (author-defined) assembly #1? 2) The pixel size is approximately the step I give to maptbx.crystal_gridding() but is not exactly isotropic. How can I enforce it as such? 3) Probably related to the question above, the box size is not cubic, I guess because of the unit cell dimensions. Since most cryo-EM programs expect maps to be cubic and have isotropic pixel sizes, I would like to enforce the final map to be sampled on a cubic grid. How can I do that? 4) Not exactly a question but what might be a bug report. When I use a model that was originally calculated based on a cryo-EM map (PDB entries I tried: 7k00, 7b75) I get the following error because the files have no crystal symmetry defined: Traceback (most recent call last): File "phenix_simulate_map.py", line 18, in <module> model.setup_scattering_dictionaries(scattering_table="electron") File "/scicore/projects/scicore-p-structsoft/ubuntu/software/Phenix/phenix-1.21-5207/modules/cctbx_project/mmtbx/model/model.py", line 2398, in setup_scattering_dictionaries self.neutralize_scatterers() File "/scicore/projects/scicore-p-structsoft/ubuntu/software/Phenix/phenix-1.21-5207/modules/cctbx_project/mmtbx/model/model.py", line 2821, in neutralize_scatterers xrs = self.get_xray_structure() File "/scicore/projects/scicore-p-structsoft/ubuntu/software/Phenix/phenix-1.21-5207/modules/cctbx_project/mmtbx/model/model.py", line 478, in get_xray_structure assert cs is not None AssertionError Thanks in advance for your help again. I hope I'm not kicking too much of a can of worms here. Best wishes, -- Ricardo Diogo Righetto Em qua., 2 de abr. de 2025 às 21:12, Alexandre OURJOUMTSEV <sacha(a)igbmc.fr> escreveu: > Hi everybody, > > > > Inversely to what Pavel wrote, just if you want to get a > limited-resolution map of the Coulomb potential (and not anything else), > eventually with a resolution that varies over the map regions, Section 5.2 > of the manuscript > > > > https://arxiv.org/abs/2412.14350 > > > > exactly explains how to do this. I guess, if this critical, Phenix teams > can routinely add such an option. > > > > With best wishes, > > > > Sacha Urzhumtsev > > > > *De :* Pavel Afonine <pafonine(a)lbl.gov> > *Envoyé :* mercredi 2 avril 2025 20:54 > *À :* James Holton <jmholton(a)lbl.gov>; phenixbb(a)phenix-online.org; > ricardorighetto(a)gmail.com > *Objet :* [phenixbb] Re: Simulate map from model > > > > Hi, > > additionally: > > - If you want an exact map (not a finite-resolution Fourier map), use: > > phenix.model_map model.pdb scattering_table=electron > > - We are close to making a multipolar model available for density > calculations, which—if I understand correctly—is what you need to simulate > Coulomb potential maps. This feature is not yet available to general Phenix > users, but if you send me the model off-list, I can generate and send the > map back to you. > > Pavel > > On 4/2/25 10:52, James Holton wrote: > > Ostensibly, all you need to do is run phenix.fmodel with > scattering_table=electron . And perhaps try to come up with what k_sol > should be for the bulk solvent density. There are caveats, of course, not > the least of which is that, last I checked, the modified scattering from > formal charges like ions vs neutral groups is not implemented. I don't > actually know of a program that handles things like charges. I've heard > rumors that someone was working on full QM calculations of electrons moving > through matter to try and get this "right", but I have not heard about any > progress for some time. > > Sorry can't be more helpful, > > -James > > On 4/2/2025 4:52 AM, Ricardo Righetto wrote: > > Hi, > > > > Apologies if I'm missing something obvious, but I was not able to find > this in the documentation: is there a PHENIX tool for simulating Coulomb > potential maps (aka "cryo-EM maps") from atomic models? > > > > I'm looking for something like the molmap > <https://www.cgl.ucsf.edu/chimerax/docs/user/commands/molmap.html> > command in ChimeraX, but more accurate. One such alternative is the > simulate program from cisTEM, but I figured PHENIX might also have > something? > > > > Thank you! > > > > -- > Ricardo Diogo Righetto > > > > _______________________________________________ > > phenixbb mailing list -- phenixbb(a)phenix-online.org > > To unsubscribe send an email to phenixbb-leave(a)phenix-online.org > > Unsubscribe: phenixbb-leave@%(host_name)s > > > > > _______________________________________________ > > phenixbb mailing list -- phenixbb(a)phenix-online.org > > To unsubscribe send an email to phenixbb-leave(a)phenix-online.org > > Unsubscribe: phenixbb-leave@%(host_name)s > >

10 months, 1 week

Re: [phenixbb] Using LigandFit to identify unknown density

by Maia Cherney

Hi Pavel, Peter, Thank you for your reply. My question is if the phenix.refine actually uses the B-factor restraints in the occupancy refinement. I did not give any restraints, so it should happen automatically? I like the idea that Peter mentioned that the restraints should make B -factors similar to surrounding molecules. Again, my question is does phenix.refine actually uses this approach? Maia Pavel Afonine wrote: > Hi Maia, > > first, I agree with Peter - the B-factor restraints should help, indeed. > > Second, I think we discussed this subject already on November 25, 2009: > > Subject: Re: [phenixbb] occupancy refinement > Date: 11/25/09 7:38 AM > > and I believe I didn't change my mind about it since that. I'm > appending that email conversation to the bottom of this email. > > Overall, if you get good 2mFo-DFc map and clear residual mFo-DFc map, > and ligand's B-factors are similar or slightly larger than those of > surrounding atoms, and refined occupancy looks reasonable, then I > think you are fine. > > Pavel. > > > On 1/27/10 2:05 PM, Maia Cherney wrote: >> Hi Pavel, >> >> I have six ligands at partial occupacies in my structure. >> Simultaneous refinement of occupancy and B factors in phenix gives a >> value of 0.7 for the ligand occupancy that looks reasonable. >> How does phenix can perform such a refinement given the occupancies >> and B factors are highly correlated? Indeed, you can >> increase/decrease the ligand occupancies while simultaneously >> increacing/decreasing their B factors without changing the R factor >> value. What criteria does phenix use in such a refinement if R factor >> does not tell much? >> >> Maia > > ******* COPY (11/25/09)************ > > > > On 11/25/09 7:38 AM, Maia Cherney wrote: >> Hi Pavel, >> >> It looks like all different refined occupancies starting from >> different initial occupancies converged to the same number upon going >> through very many cycles of refinement. >> >> Maia >> >> >> Pavel Afonine wrote: >> >>> Hi Maia, >>> >>> the atom parameters, such as occupancy, B-factor and even position >>> are interdependent in some sense. That is, if you have somewhat >>> incorrect occupancy, that B-factor refinement may compensate for it; >>> if you misplaced an atom the refinement of its occupancy or/and >>> B-factor will compensate for this. Note in all the above cases the >>> 2mFo-DFc and mFo-DFc maps will appear almost identical, as well as >>> R-factors. >>> >>> So, I think your goal of finding a "true" occupancy is hardly >>> achievable. >>> >>> Although, I think you can approach it by doing very many refinements >>> (say, several hundreds) (where you refine occupancies, B-factors and >>> coordinates) each refinement starting with different occupancy and >>> B-factor values, and make sure that each refinement converges. Then >>> select a subset of refined structures with similar and low R-factors >>> (discard those cases where refinement got stuck for whatever reason >>> and R-factors are higher) (and probably similar looking 2mFo-DFc and >>> mFo-DFc maps in the region of interest). Then see where the refined >>> occupancies and B-factors are clustering, and the averaged values >>> will probably give you an approximate values for occupancy and B. I >>> did not try this myself but always wanted to. >>> >>> If you have a structure consisting of 9 carbons and one gold atom, >>> then I would expect that the "second digit" in gold's occupancy >>> would matter. However, if we speak about dozen of ligand atoms >>> (which are probably a combination of C,N,O) out of a few thousands >>> of atoms of the whole structure, then I would not expect the "second >>> digit" to be visibly important. >>> >>> Pavel. >>> >>> >>> On 11/24/09 8:08 PM, chern wrote: >>> >>>> Thank you Kendall and Pavel for your responces. >>>> I really want to determine the occupancy of my ligand. I saw one >>>> suggestion to try different refinements with different occupancies >>>> and compare the B-factors. >>>> The occupancy with a B-factor that is at the level with the average >>>> protein B-factors, is a "true" occupancy. >>>> I also noticed the dependence of the ligand occupancy on the >>>> initial occupancy. I saw the difference of 10 to 15%, that is why I >>>> am wondering if the second digit after the decimal point makes any >>>> sence. >>>> Maia >>>> >>>> ----- Original Message ----- >>>> *From:* Kendall Nettles <mailto:[email protected]> >>>> *To:* PHENIX user mailing list <mailto:[email protected]> >>>> *Sent:* Tuesday, November 24, 2009 8:22 PM >>>> *Subject:* Re: [phenixbb] occupancy refinement >>>> >>>> Hi Maia, >>>> I think the criteria for occupancy refinement of ligands is >>>> similar to a decision to add an alt conformation for an amino >>>> acid. I don’t refine occupancy of a ligand unless the difference >>>> map indicates that we have to. Sometimes part of the igand may be >>>> conformationally mobile and show poor density, but I personally >>>> don’t think this justifies occupancy refinement without evidence >>>> from the difference map. I agree with Pavel that you shouldn’t >>>> expect much change in overall statistics, unless the ligand has >>>> very low occupancy., or you have a very small protein. We >>>> typically see 0.5-1% difference in R factors from refining with >>>> ligand versus without for nuclear receptor igand binding domains >>>> of about 250 amino acids, and we see very small differences from >>>> occupancy refinement of the ligands. >>>> >>>> Regarding the error, I have noticed differences of 10% percent >>>> occupancy depending on what you set the starting occupancy before >>>> refinement. That is, if the starting occupancy starts at 1, you >>>> might end up with 50%, but if you start it at 0.01, you might get >>>> 40%. I don’t have the expertise to explain why this is, but I >>>> also don’t think it is necessarily important. I think it is more >>>> important to convince yourself that the ligand binds how you >>>> think it does. With steroid receptors, the ligand is usually >>>> planer, and tethered by hydrogen bonds on two ends. That leaves >>>> us with with four possible poses, so if in doubt, we will dock in >>>> the ligand in all of the four orientations and refine. So far, we >>>> have had only one of several dozen structures where the ligand >>>> orientation was not obvious after this procedure. I worry about a >>>> letter to the editor suggesting that the electron density for the >>>> ligand doesn’t support the conclusions of the paper, not whether >>>> the occupancy is 40% versus 50%. >>>> >>>> You might also want to consider looking at several maps, such as >>>> the simple or simulated annealing composite omit maps. These can >>>> be noisy, so also try the kicked maps ( >>>> >>>> http://www.phenix-online.org/pipermail/phenixbb/2009-September/002573.html), >>>> >>>> >>>> <http://www.phenix-online.org/pipermail/phenixbb/2009-September/002573.html%…,> >>>> >>>> which I have become a big fan of. >>>> >>>> Regards, >>>> Kendall Nettles >>>> >>>> On 11/24/09 3:07 PM, "chern(a)ualberta.ca" <chern(a)ualberta.ca> >>>> wrote: >>>> >>>> Hi, >>>> I am wondering what is the criteria for occupancy >>>> refinement of >>>> ligands. I noticed that R factors change very little, but the >>>> ligand >>>> B-factors change significantly . On the other hand, the >>>> occupancy is >>>> refined to the second digit after the decimal point. How can >>>> I find >>>> out the error for the refined occupancy of ligands? >>>> >>>> Maia >>>> > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > >

16 years

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